Skip to another splice site:
1  
 5'  3'   		2  
 5'  3'   		3  
 5'  3'   		4  
 5'  3'   		5  
 5'  3'   		6  
 5'  3'   		7  
 5'  3'   		8  
 5'  3'   		9  
 5'  3'   		10  
 5'  3'   

Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtataacacatttgacacagttatacacctataccattagtgagcaatgcattattttcatgtaggataacataaatattcaaccttcagGTGTATTTTGAGTCAGAAGAAGCGAAAGCTTGCATTGTAACCTGTGGAGGCCTTTGCCCTGGGCTCAATACTGTCATCAGAGAGTTGGTTTGTGGCTTGT

Basic information

species Zea mays
transcript GRMZM5G879882_T02
intron # 4
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM5G879882_T03 (Zea mays), 3'ss of exon 4
lower sequence: LOC_Os01g53680.1 (Oryza sativa), 3'ss of exon 4
gtataacacatttgacacagttatacacctat-accattagtgagcaatgcattattttcatgtaggataacataaatattcaacctt---cagGTGTATTTTGAGTCAGAAGAAGCGAAAGCTTGCATTGTAACCTGTGGAGGCCTTTGCCCTGGGCTCAATACTGTCATCAGAGAGTTGGTTTGTGGCTTGT
|||  |  | || ||      ||||  ||||| | ||||   | ||| |||||||    ||| |||| | ||| ||||  ||||   |   |||||||| || ||||||||||| |  ||||| |||||||||||||| |||||||||||||||||||| ||||| ||||| ||||||||||| || |||||||
gtaggatgccttgga------tatatgcctattatcatttaggggca-tgcattacccacatttaggctgacacaaattctcaaatcttatcagGTGTACTTCGAGTCAGAAGATGTCAAAGCATGCATTGTAACCTGCGGAGGCCTTTGCCCTGGGCTAAATACGGTCATTAGAGAGTTGGTGTGCGGCTTGT

upper sequence: GRMZM5G879882_T03 (Zea mays), 3'ss of exon 4
lower sequence: Vv04s0008g00520.t01 (Vitis vinifera), 3'ss of exon 4
gtataacacatttgacacagttatacacctataccattagtgagcaatgcattattttcatgtaggataacataaatattcaaccttcagGTGTATTTTGAGTCAGAAGAAGCGAAAGCTTGCATTGTAACCTGTGGAGGCCTTTGCCCTGGGCTCAATACTGTCATCAGAGAGTTGGTTTGTGGCTTGT
       || | |    |  || |     |  |     | |||   ||| || ||    || ||  ||   |    || |      ||||||||||||||||||||| |||| | | || || |||||||| ||||| || || |||||||||||||| || |||||||| ||  | || |||||| | |
-----gtacgtcttcttcttttctcgcagtgcaagtggaatga-tgatgtatcatgcatatttactatgtaacttttaat-ggtgctcagGTGTATTTTGAGTCAGATGAAGTGCACGCATGTATTGTAACATGTGGTGGTCTGTGCCCTGGGCTCAACACAGTCATCAGGGAAATTGTGTGTGGCCTTT
















Mapped EST sequences

Showing partial alignments of ESTs and genomic sequences. See full alignments


 ATGC     EST sequence
 ATGC     genomic sequence (exon)
 ATGC     genomic sequence (truncated intron)


EST: gi|8367787|gb|BE050732.1|BE050732
EST:     AGAACAGTCCACGAGGAGTTCACTTCCGTCGTGCTGGACCTCGTCAGAGG                         GTGTATTTTGAGTCAGAAGAAGTGAAAGCTTGCATTGTAACCTGTGGAGGC
genomic: AGAACAGTCCACGAGGAGTTCACTTCCGTCGTGCTGGACCTCGTCAGAGGgtataacaca ... caaccttcagGTGTATTTTGAGTCAGAAGAAGCGAAAGCTTGCATTGTAACCTGTGGAGGC
EST: gi|87153557|gb|DY398346.1|DY398346
EST:     AGAACAGTCCACGAGGAGTTCACTTCCGTCGTGCTGGACCTCGTCAGAGG                         GTGTATTTTGAGTCAGAAGAAGTGAAAGCTTGCATTGTAACCTGTGGAGGC
genomic: AGAACAGTCCACGAGGAGTTCACTTCCGTCGTGCTGGACCTCGTCAGAGGgtataacaca ... caaccttcagGTGTATTTTGAGTCAGAAGAAGCGAAAGCTTGCATTGTAACCTGTGGAGGC
EST: gi|28873675|gb|CB329630.1|CB329630
EST:     AGAACAGTCCACGAGGAGTTCACTTCCGTCGTGCTGGACCTCGTCAGAGG                         GGGTATTTTGAGTCAGAAGAAGCGAAAGCTTGCATTGTAACCTGTGGAGGC
genomic: AGAACAGTCCACGAGGAGTTCACTTCCGTCGTGCTGGACCTCGTCAGAGGgtataacaca ... caaccttcagGTGTATTTTGAGTCAGAAGAAGCGAAAGCTTGCATTGTAACCTGTGGAGGC
EST: gi|19436208|gb|BM952618.1|BM952618
EST:     AGAACAGTCCACGAGGAGTTCACTTCCGTCGTGCTGGACCTCGTCAGAGG                         GTGTATTTTGAGTCAGAAGAAGTGAAAGCTTGCATTGTAACCTGTGGAGGC
genomic: AGAACAGTCCACGAGGAGTTCACTTCCGTCGTGCTGGACCTCGTCAGAGGgtataacaca ... caaccttcagGTGTATTTTGAGTCAGAAGAAGCGAAAGCTTGCATTGTAACCTGTGGAGGC


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

attagtgagcaatgcattattttcatgtaggataacataaatattcaaccttcagGTGTATTTTGAGTCAGAAGAAGCGAAAGCTTGCATTGTAACCTGTGGAGGCCTTTGCCCTGGGCTCAATACTGTCATCAGAGAGTTGGTTTGTGGCTTGT
                             ggataac  putative branch site (score: 3)
                                                ccttc  putative PPT
                               ataacataaatattca  TA-rich tract